We propose that both human cancers and birth defects are caused by defects in stem cell pluripotency and self-renewal. Tumor formation is theorized to often be the result of oncogenic transformation of normal stems into cancer stem cells. Birth defects are due to disruptions of the pluripotency and self-renewal of stem cells, including inner cell mass cells that are very similar embryonic stem cells (ESC). The molecular mechanisms that cause these stem cell changes leading to human disease remain an open question, but the myc gene family is linked to both human birth defects and cancers suggesting Myc proteins may play key roles in both diseases. We are particularly interested in the specific roles that Myc proteins play in stem cells that lead to human birth defects and cancers. The proposed studies will address the issue of how a single class of proteins, the Myc family, can be so essential for stem cell biology and embryogenesis at normal levels, but in excess cause cancer and produce induced pluripotent stem (iPS) cells. Using proteomics, we have identified three novel Myc cofactors that may direct its function in ESC: histone deacetylases (HDACs); the DNA methyltransferases, DNMT3; and the ESC-specific transcription factor, UTF1. Myc proteins have no known cofactors in ESC or iPS cells, representing a serious gap in the field that our work will bridge. By analyzing the biochemical properties of these protein-protein interactions as well as the nature of how they form on DNA to regulate transcription, the proposed work will provide key insight into Myc function in maintaining pluripotency in ESC and establishing pluripotency in iPS cells. Innovative aspects of the proposal include a new model of how Myc functions as transcription factor including a widespread, repressive function, novel proteomics studies on Myc complexes in stem cells, studies on iPS cells, and analyzing the function of UTF1. When these studies are complete we will have a clearer understanding of the molecular mechanisms that control pluripotency as well as human development and how when disrupted these events lead to human disease.